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NM_000290.4(PGAM2):c.707A>C (p.Glu236Ala)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jul 4, 2021)
Last evaluated:
Jul 12, 2020
Accession:
VCV000440991.9
Variation ID:
440991
Description:
single nucleotide variant
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NM_000290.4(PGAM2):c.707A>C (p.Glu236Ala)

Allele ID
434619
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7p13
Genomic location
7: 44062819 (GRCh38) GRCh38 UCSC
7: 44102418 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.44102418T>G
NC_000007.14:g.44062819T>G
NG_013016.1:g.7769A>C
... more HGVS
Protein change
E236A
Other names
-
Canonical SPDI
NC_000007.14:44062818:T:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (G)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00025
The Genome Aggregation Database (gnomAD), exomes 0.00070
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00031
Exome Aggregation Consortium (ExAC) 0.00080
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00038
Links
ClinGen: CA4236494
dbSNP: rs140230479
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 3 criteria provided, multiple submitters, no conflicts Jul 12, 2020 RCV000509297.4
Uncertain significance 1 criteria provided, single submitter May 1, 2020 RCV001200533.2

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
DBNL - - GRCh38
GRCh37
- 94
PGAM2 - - GRCh38
GRCh37
- 94

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jul 12, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type X
Allele origin: germline
Invitae
Accession: SCV001107608.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type X
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001325561.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(May 01, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001371521.4
Submitted: (Jul 04, 2021)
Evidence details
not provided
(-)
no assertion provided
Method: phenotyping only
Glycogen storage disease X
Allele origin: unknown
GenomeConnect, ClinGen
Accession: SCV000607023.1
Submitted: (Aug 22, 2017)
Evidence details
Comment:
GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs140230479...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 07, 2021